Naruto the Ultimate Experiment
by Bahamutsoulking
Summary: What if Naruto was taken from Konoha at age 5 and gets experimented on by Orochimaru, how will Konoha take Naruto's disappearance, will they feel guilty for their sins, how will Konoha right all of their wrongs. Smart/Powerful Naruto, living Kushina, harem, Sakura/Civilian Council bashing, evil Danzo, good Akatsuki/Elders/Kabuto, Blood and Gore


Hello and welcome, this will be a very different kind of fanfic which is Naruto getting experimented on by Orochimaru, Orochimaru will inject DNA from other warriors that he fought and snagged samples from into the poor boy.

I was inspired by fanfics that had Orochimaru injecting the DNA of the Akatsuki along with others including his own DNA into Naruto himself, and I came up with an idea, why not inject any Kekkei Genkai that interested Orochimaru into Naruto, if you guys want you can make up some Kekkei Genkais of your own and I'll even let you invent the jutsu based off of them. I hope you guys enjoy this fanfic, Sasuke will be good.

The main villains are Orochimaru, Madara, Danzo and Obito.

How will Naruto handle life after what Orochimaru will do to him, here we go!

harem: Hinata/Kin/Guren/Tayuya/Karin/Mei/Kurotsuchi/Ryuuzetsu/Karui/Anko/Yugao/Konan/Shion/Kurenai/Fu/Yugito/Yakumo/Pakura/Koyuki/Haruna/Toki/Ameyuri

'Thoughts'

"Jutsu"

" _Flashback_ "

" **Kyuubi** "

* * *

Chapter 1: The Experiment Begins

After 5 year since the Kyuubi attacked, we find the crazy scientist Orochimaru roaming the Elemental Nations wearing an Akatsuki robe, searching for warriors with interesting Kekkei Genkais to take samples from, he already has taken the cells of Hashirama Senju, Madara Uchiha and Izuna Uchiha as well as others with Kekkei Genkai that interested him, including the tailed beasts (excluding Kyuubi), Orochimaru wanted to merge 3 different Uchiha samples that had the Mangekyo Sharingan together to make 3 different Mangekyo Sharingan abilities into one super powerful Eternal Mangekyo Sharingan he just needs one more DNA sample from one different Uchiha.

"Alright, now I need DNA samples of the members of the Akatsuki, and that is gonna be difficult." said Orochimaru, and Orochimaru decides to get a sample from Hidan first, the Jashinist is granted immortality for doing the sacrifice to Jashin himself.

Orochimaru got a sample of Hidan's blood into a vile with a label on it, and preserves the blood, Orochimaru grins like a madman and says "One down, Eight to go", and Orochimaru then spars with Kisame and after the spar Orochimaru knows that getting DNA from Samehada is gonna be difficult because the Sharkskin is very sharp and will rip you to shreds and he gets a metal stick and gets the scale, preserves it and puts it into the 2nd labeled vile.

"Two down, Seven to go" said Orochimaru, another time, he spars with Deidara and gets a blood sample into another labeled vile after he preserves it, "Three down, Six to go" said Orochimaru with a wicked grin on his face.

* * *

Orochimaru then goes to a tree and sees Konan's paper butterflies fluttering and throws a senbon at one and gets it, he gets the sample into another labeled vile, "Four down, Five to go" said Orochimaru.

He finds the unsuspecting Zetsu and takes a strand of Zetsu's hair and quickly pulls back as the mouth of the plant-like being clamps shut and opens again and asks "What are you doing?", and Orochimaru says "I saw a fly and it was going to bother you and I snatched the fly before it can do it.", and Zetsu accepts the answer "A little warning next time" he said and Orochimaru says "Sure" and they walk their ways and Orochimaru gets the sample into another labeled vile, "Five down, Four to go" he said.

He then goes and spars with Kakuzu and on one of the attacks Orochimaru grabbed some of Kakuzu's threads and pulls his hand into his cloak, after the spar is done Orochimaru got the threads into the empty vile, "Six down, Three to go" said Orochimaru with a victorious grin.

Orochimaru found Sasori and sparred with him and manages to get a sample from Sasori and gets the sample into a empty vile, Orochimaru grins evily and says "Seven down, Two to go", and Orochimaru finds Pein and manages to get a hair sample from him and gets the hair into the empty vile, "Eight down, One to go" Orochimaru said.

'Almost there' he thought, and Orochimaru finds Itachi and fights him and this time Orochimaru gets injured from the fight and still got the blood sample from Itachi and grins in victory, "Immortality will be mine at last, and the three Uchiha samples will get merged together and become the Ultimate Sharingan." said Orochimaru.

* * *

Orochimaru gets to the Sound Village and prepares for his experiment, and after 100 test subjects one by one they all die, Orochimaru is furious that nothing is working to create the perfect vessel.

Orochimaru then sends for his right hand man Kabuto Yakushi, "Kabuto, it has been the 100th test subject and nothing is working, tell me what can we do to get this to work." asked Orochimaru.

Kabuto says "Maybe we need to find someone that can take all these samples into their body at once so it can be easy to do this.", and Orochimaru looks at him and asks "What do you suggest?", and Kabuto grins and says "How about the Jinchuuriki for the Kyuubi".

"Any reason on suggesting the Kyuubi Jinchuuriki?" asked Orochimaru again, "The Kyuubi will prevent death to the boy, it will make things much easier, it's perfect." said Kabuto, "If we extract the Kyuubi from him, then he will survive because of Hidan's DNA." said Orochimaru in surprise, "Yes" answered Kabuto.

Orochimaru grins madly and says "Fetch him", and Kabuto says "As you wish".

* * *

Kabuto goes to Konoha and puts on a Konoha headband and gets through the gate easily, he is searching for the Kyuubi Jinchuuriki and hears some stupid villagers shouting 'kill the demon' and that is when he smirks.

'I have finally found him.' thought Kabuto, he gets on a roof and sees a 5 year old blonde headed boy running from a mob and hides in a box big enough to keep him hidden.

The villagers run passed the box and Naruto peaks out and sees that the coast is clear and he gets home and he sees someone and asks "Who are you?", "I am Kabuto Yakushi, and what is your name?" asked Kabuto.

"My name is Naruto Uzumaki." said Naruto, and Kabuto asks "Do you want to be able to defend yourself from those bloodthirsty savages?", and Naruto is surprised and says "I wanna be able to defend myself, but nobody will train me.", and Kabuto says "Don't worry Naruto, there will be people who will train you.".

Kabuto then puts Naruto in a sleeping genjutsu and injects him with a chemical that will keep Naruto asleep and Kabuto gets him into a sack and sneaks out of the village with an unconcious Naruto.

* * *

(Sound Village)

Kabuto gets to the Sound Village and gets to Orochimaru, "How was the retrieval?" asked Orochimaru, Kabuto smirks and says "Success" as he gets Naruto out of the sack, Orochimaru smiles and says "Excellent, we will now start the experiments.".

Kabuto picks up Naruto and puts him on a operating table and straps him down, and hooks up medical machines to Naruto along with putting a breathing mask on him, "Are we doing the Akatsuki DNA first?" asks Kabuto, and Orochimaru says "No, we will start with Kimimaro's DNA, we will see if the boy will get the Kaguya Kekkei Genkai.", and Kabuto says "As you wish Orochimaru-sama".

Kabuto prepares the injection and injects the Kaguya DNA into Naruto's arm, after a while of waiting, Kabuto takes a drop of Naruto's blood to find out if Naruto gained the bloodline, "Ok, time to see if it worked." he said, and he gets the results, "It worked" he said in glee, and goes to tell Orochimaru, "Well?" asked Orochimaru, and Kabuto grins and says "It's a success, Naruto now has the Kaguya Kekkei Genkai.".

Orochimaru grins like a madman and says "Excellent, now he needs to recover and then we can inject him with Juugo's DNA so he can adapt the other powers that we will inject into him just in case it starts to become a failure.", and Kabuto says "That's a wise plan, how long til we inject Juugo's DNA?" and Orochimaru says "A week".

* * *

(Leaf Village)

Meanwhile back in Konoha, Sarutobi learns about Naruto's disappearance and sends Anbu to find Naruto, and they have no luck at all. Sarutobi then calls a council meeting, as the council members are in the room, Hiruzen comes and takes a seat in the Hokage chair.

"Who called for this meeting?" asked a civilian council member, and Sarutobi says "I did", and Danzo asks "Is there a reason you called for this meeting Hiruzen?", and Koharu says "Yes, is there a reason?", and Sarutobi says "Naruto Uzumaki has suddenly disappeared from Konoha without a trace.", the shinobi council and the elders (minus Danzo) pale from this, the civilian council cheer that Naruto is out of the village.

"Yay, the demon is out of the village now we can have peace for once." says a stupid civilian, and then massive killing intent floods the room, the civilian side look at Sarutobi in fear, "Fools, Naruto is the son of Minato Namikaze the Yondaime Hokage and Kushina Uzumaki the Red Death, Naruto was born before the Kyuubi rampaged." snarled Sarutobi, and everyone except the shinobi and elders pale at this, everyone who knows about Naruto's heritage smirk at the looks of the civilian's faces.

"WHAT?, THERE IS NO WAY THAT THE DEMON-BRAT IS THE SON OF OUR GREAT YONDAIME." shrieked the stupidest pink-haired council member.

"So, you refuse to believe that the Yondaime has a son even though the village treated him like dirt for carrying the burden of being the host of the Kyuubi no Kitsune." said Homura smugly, and the civilians get less and less confident by the second, "Everyone knows that no matter how hard you try, you cannot escape the truth." he finishes.

"Meeting dismissed." said Hiruzen, and everyone leaves the room except the Hokage and elders, "Anbu" said Hiruzen and some anbu appear, "Naruto Uzumaki Namikaze has disappeared without a trace, your mission is to find Naruto and get him back home." Sarutobi orders, "Yes sir" they reply and they shunshin out to find Naruto.

'We need to find Naruto before Kushina wakes up from her coma and fast, otherwise that would be bad.' thought Hiruzen grimly.

* * *

(Sound Village, a week later)

Back in Orochimaru's secret lab in Iwa country, after a week of letting Naruto recover, Orochimaru says "Ok, it's been a week, now do Jugo's DNA.", "Yes Orochimaru-sama" says Kabuto.

In a different part of the labs, the sound 5 along with others like Kin, Zaku, Dosu, Karin and Guren are talking to eachother, when they heard that Orochimaru found a new lab-rat which was Naruto, they have been curious about Naruto ever since.

"This Naruto kid is supposed to be Orochimaru-sama's new body, why is he choosing a kid?" asked Kidomaru, and Kimimaro says "He is to replace me as Orochimaru-sama's new host, I heard that he is being experimented on even right now.".

"I heard that he is the Kyuubi Jinchuuriki." said Guren, shocking everyone even Kimimaro, "No way" said Sakon in shock, and Guren says "Way", "Why the fuck would Orochimaru need the Kyuubi Jinchuuriki as a lab-rat?" asked Tayuya in a annoyed tone, and Jirobo answers "He's taking advantage of the Kyuubi to have him survive all the experiments that he'll be going through.".

"You are correct Jirobo." said Kabuto as they turn to him, "Orochimaru-sama wants to inject Jugo's DNA into Naruto's body so he can adapt the DNA that will be injected into him." Kabuto informs them, "If you want to see him, come with me." said Kabuto, and they go with Kabuto to finally see the kid.

Kabuto and the others go into the room where Naruto is being held, they go in and see the blond 5 year old boy strapped to the operating table with medical equipment hooked up to him, "So this is the boy, he's the same age as us." said Tayuya, "Yes, this is Naruto Uzumaki Namikaze." said Kabuto, "He's the son of the Yondaime Hokage Minato Namikaze." said Guren in surprise as the others except Kabuto are surprised as well.

"Yes" said Kabuto, "Why would the Yondaime Hokage seal the Kyuubi into his own son?" asked Kin, "He chose to save Konoha by sealing the Kyuubi into his son, he wanted his son to be seen as a hero for keeping the beast at bay, but that dying wish was never honored by everyone of Konoha, except a couple of people, he was starved, beaten, burned alive, buried alive and even crucified by the villagers who refuse to accept him." answered Kabuto.

Everyone had different reactions, Kin covered her mouth in horror with tears in her eyes while Karin, Tayuya and Guren start to cry tears of sadness when they heard Naruto's past, the guys get angry at this, Kimimaro growls, "They're like savage wolves that prey on another's pain and suffering.".

Kimimaro may be a Kaguya, but even he wouldn't go that far to make a child suffer even though he doesn't like violence, "Yes, we already injected Kimimaro's DNA and he gained the Kaguya Bloodline." said Kabuto, and Kimimaro for the first time in years felt happy that Naruto gained his clan's Kekkei Genkai so he would be able to teach him how to use it properly.

Kabuto gets the injector ready and says "Ok, here we go.", and he injects Naruto with Jugo's DNA, as they watch and wait for a while like the other time, Kabuto then takes a drop of Naruto's blood and checks for any signs of Jugo's bloodline, "This might take some time." said Kabuto.

After 3 minutes of examining Naruto's blood, Kabuto gets the results "This one worked too." Kabuto said in surprise.

Kabuto goes to Orochimaru, "Orochimaru-sama, the injection for Jugo's DNA is a success." he said, "Excellent, now to let him recover for a week until we inject him with the DNA of the Yuki clan." Orochimaru ordered, "As you wish Orochimaru-sama." said Kabuto.

* * *

(Back at the Leaf Village)

Hiruzen is in the hospital walking to the room where Kushina is being kept until she recovers from a coma, 'Minato-kun, Kushina-chan forgive me for not protecting your son.' he thought regretfully.

Then he sees a doctor trembling on the ground in fear outside of Kushina's room, "What's wrong?" asked Hiruzen, "She's awake." answered the doctor, Hiruzen's eyes widen and he goes in.

What meets him is an enraged Kushina beating on doctors and nurses, "Kushina?" asked Hiruzen, and the red headed woman turns to him and asked in a sinister voice "Sarutobi, where...is...Naruto, WHERE IS MY BABY?".

'Too late, now I'm in trouble' thought Hiruzen.

(To be continued)

* * *

There you have it folks, Naruto got captured by Orochimaru and is now being used as a lab-rat, and after 2 successful DNA injections, Orochimaru now needs to turn him into the perfect host.

What will happen when Konoha discover that it was Orochimaru who is responsible for Naruto's sudden disappearance.

* * *

Here are the Kekkei Genkais that Orochimaru snagged:

Dead Bone Pulse [Injected]

Ice Style Kekkei Genkai

Sharingan

Byakugan

Rinnegan

Wood Style Kekkei Genkai

Crystal Style Kekkei Genkai

Lava Style Kekkei Genkai

Boil Style Kekkei Genkai

Magnet Style Kekkei Genkai

Jugo's Clan's Kekkei Genkai [Injected]

Particle Style Kekkei Genkai

* * *

Now for the power the Akatsuki possessed:

Hidan (Jashinism)

Deidara (Explosion Kekkei Genkai)

Itachi Uchiha (Sharingan)

Nagato Uzumaki (Rinnegan)

Sasori (Puppet Master Jutsu)

Kisame Hoshigaki (Samehada, {took some scales})

Orochimaru (Snake Sannin) [I know he's not a member anymore but I decided to have his DNA into Naruto. -_-']

Zetsu (Wood Style Jutsu)

Konan (Paper Jutsu)

Kakuzu (Self repairing threads)

* * *

What will become of Konoha when Kushina finds out that her son was disrespected for something he had no control over.

How will Naruto use his new-found power when he wakes up.

What will happen when Akatsuki find out about the experiments that Orochimaru is putting poor Naruto through.

Stay Tuned for Chapter 2!

Please don't flame, I really don't like it that people flame, but I do appreciate it when you give me support and some ideas for the fanfiction.


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